godzilla wins easily under these circumstances.
the size difference is the major deciding factor here. if they could be scaled appropriately that would easily level the playing field.
so first lets scale them appropriately. lets make kong twice as big and then shrink gozilla down a bit so that they are the same shoulder height. i believe even with that rescaling it leaves godzilla substantially more mass.
lets try to ignore physics and how their physiology would have to be augmented to allow these animals to cope with their sheer mass.
so lets look at primary attributes in this situation, off the top of my head...
king kong is going to have dexterity, agility and intelligence.
godzilla is going to have durability, strength and instinct.
with kongs dexterity that allows him to climb more readily and in conjunction with his intelligence, allows him to utilize the environment to his advantage ie. car sheild, or anything as a projectile. his gorilla physiology and smaller build is going go give him greater agility being able to react or avoid attacks with less room for error.
godzilla im simply assuming would have a thicker hide hence the durability but i also lump all those gnarly scales and claws in with this attribute. her strength goes hand in hand with not only larger mass but the fact that we assume she is a reptile and unlike theropods cold blooded. with being cold blooded you have little endurance but excel with burts of speed. (something i should add to the primary attributes endurance and burst damage respectively.)reptilian instinct is going to allow her greater speed in that there is little thought involved just millions of years of evolutionary programming.
im hoping some of you can chime in with additional attributes or amend what i have portrayed here. for example should godzilla be considered a theropod? obviously then she wouldnt just be a mutated marine iguana. we may have to change the story line a bit. maybe instead of being the product of nuclear tests rather may have come from the island kong did, or make it not just one island but a chain. because if you didnt know that one sank.
i highly recommend "World of Kong"
http://www.amazon.com/The-World-Kon...LGTA/ref=sr_1_1?ie=UTF8&qid=1332121215&sr=8-1
it has a lot of concept art, and theres even a page or two on chameleons (though i dont know how they would have made it that far into the pacific)
if youre a fan of dinosaurs and megafauna its a MUST HAVE
its been a LONG time but i used to be obsessed with the old school godzilla movies. but if i recall correctly kong from the old movies had this ability to absorb electricity and it made him (super saiyan) stronger. and godzilla had the flame breath. so we should incorperate those later if anyone cares enough to hash out strengths and weaknesses before we add their super powers. regardless they kind of equal each other out.
plus he's big and bad and could totally bite kingkongs face off...than again in the movie he breaks the t-rex's jaw. i was so sad 
